dotools_py.get.dge_results

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dotools_py.get.dge_results#

dotools_py.get.dge_results(adata, key='rank_genes_groups', min_log2fc=None, padj_cutoff=None, max_log2fc=None)[source]#

Extract DEGs from AnnData object.

This function extract the results of the differential gene expression analysis results from the uns attribute of an AnnData object.

Parameters:
adata AnnData

Annotated data matrix.

key str (default: 'rank_genes_groups')

Key in uns with DGE results.

min_log2fc float (default: None)

Minimum log2-foldchange.

max_log2fc float (default: None)

Maximum log2-foldchange.

padj_cutoff float (default: None)

Cutoff for the adjusted p-value.

Return type:

DataFrame

Returns:

Returns a DataFrame with the results of the differential gene expression analysis generated from rank_genes_groups.

Example

>>> import dotools_py as do
>>> adata = do.dt.example_10x_processed()
>>> do.tl.rank_genes_groups(adata, groupby="condition")
>>> df = do.get.dge_results(adata)
>>> df.head(5)
         group GeneName  wilcox_score  ...          padj  pts_group   pts_ref
0  disease   ZNF331     15.936105  ...  6.586861e-54   0.650000  0.096154
1  disease      EZR     15.871257  ...  9.274798e-54   0.866667  0.367308
2  disease     EIF1     14.823599  ...  6.361829e-47   0.994444  0.994231
3  disease     SRGN     14.721976  ...  2.155706e-46   0.922222  0.636538
4  disease     EGR1     12.330428  ...  1.916262e-32   0.316667  0.011538
[5 rows x 8 columns]
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